Recent Releases of pyfastx
pyfastx - v2.0.0
- Added support for file name with wide char ( #66 )
- Added support for specifying index file path ( #45 )
- Added support for more characters in DNA sequence
- Added reverse complement function for DNA conversion ( #69 )
- Improved the performance of kseq library ( #68 )
- Optimized gzip index importing and saving without temp file
- Fixed segmentation fault when using sequence composition ( #67 )
- Fixed memory leak in Fastq read quality integer ( #70 )
- Fixed zlib download url broken error when building
- C
Published by lmdu over 2 years ago
pyfastx - v0.9.0
- Added support for Python3.10, 3.11
- Added support for aarch64 and musllinux ( #34 )
- Added using tab as fasta sequence name splitter
- Fixed repeat sequence comment error ( #37 #49 )
- Fixed the quality score parsing error from fastq ( #44 )
- Fixed the reference of sequence returned from function ( #36 )
- C
Published by lmdu about 3 years ago
pyfastx - v0.8.2
- Fixed sample segfault error caused by fastq iteration error ( #28 )
- Fixed fastq iteration segfault error with full_name=True ( #26 )
- Fixed gzip index import error in multiple processes ( #25 )
- Fixed all objects iteration to support built-in next function
- C
Published by lmdu about 5 years ago
pyfastx - v0.8.0
- Added Fastx object as a simple sequence iterator
- Added FastqKeys object to obtain read names
- Added full_name option to Fastq object
- Added support for Python 3.9
- Fixed Fasta object error identifier order
- Optimized speed of containing test and iteration
- Changed Identifier object to FastaKeys object
- C
Published by lmdu about 5 years ago
pyfastx - v0.7.0
- Added support for extracting flank sequences
- Added support for indexing super large gzip file
- Reduced memory consumption when building gzip index
- Improved the speed of random access to reads from fastq
- Fixed sequence dealloc error cuasing no fasta delloc trigger
- Fixed fastq max and min quality score return value
- C
Published by lmdu over 5 years ago
pyfastx - v0.6.15
- Fixed key_func error caused by free operation ( #19 )
- Fixed full name error when reading sequence without whitespace in names ( #19 )
- Fixed a hidden bug in fasta/q iteration when reading attributes (not seq)
- Fixed fasta/fastq size and sequence count error on Windows when parsing large file
- Fixed zlib 2gb and 4gb limit on windows x64 to support large file
- Reduced seek point span size to speedup random access from gzip file
- C
Published by lmdu over 5 years ago
pyfastx - v0.6.10
- Improved the speed of sequence reading ( #12 )
- Improved the speed of sequence line iteration
- Added avglen, minlen, maxlen, minqual and maxqual to Fastq object
- Fixed read retrieval error ( #13 )
- Fixed some hidden memory leaks
- Changed fastq index file structure to save more information
- C
Published by lmdu almost 6 years ago
pyfastx - v0.6.9
- Added buffreader to improve speed for reading from gzipped file
- Added extract subcommand to extract sequences from fasta/q file
- Added build subcommand to just build index
- Changed info subcommand output to a tab seperated table
- Changed Fastq object composition parameter to full_index
- C
Published by lmdu almost 6 years ago
pyfastx - v0.6.3
- Added .raw attribute to sequence object to get seq raw string ( #4 )
- Added .raw attribute to read object to get read raw string ( #4 )
- Added .description to read object to get full header line ( #4 )
- Added iteration for sequence object from FASTA object ( #3 )
- Added iteration for tuple from FASTQ object
- Changed FASTA class parameter composition to full_index
- C
Published by lmdu about 6 years ago
pyfastx - v0.6.0
- Fixed FASTA object parameter error
- Fixed identifier sprintf warning
- Fixed fasta description end \r retained
- Fixed error byte length when slice sequence
- Removed support for python2.7 and python3.4
- Removed python2 compat
- Disabled export gzip index when building memory index
- C
Published by lmdu about 6 years ago
pyfastx - v0.5.9
- Added get longest and shortest sequence object
- Added composition argument to speedup getting GC content
- Added memory index to keep index in memory rather than local file
- Fixed command line error ( #2 )
- Changed sqlite to higher version
- Removed journal_mode OFF
- Speedup index building
- C
Published by lmdu over 6 years ago
pyfastx - v0.5.0
- Added support for python 2.7 and 3.4
- Added command line tool to manipulate fasta and fastq file
- Added gzip attribute to fasta and fastq object to check whether compressed
- Added sort function for identifier object
- Fixed python bool argument parsing error caused by uint16_t
- Fixed identifier sort key initialization
- C
Published by lmdu over 6 years ago
pyfastx - v0.3.0
- Added read sequence from fasta file line by line
- Added support for calculating assembly N50 and L50
- Added support for calculating median and average length
- Added support for getting longest and shortest sequence
- Added support for calculating counts of sequence
- Removed support for Python34
- C
Published by lmdu over 6 years ago